Nunes joined the Society of Jesus (Jesuits) in 1543. In 1555 he was appointed bishop of Nicaea and was consecrated bishop at Goa in 1560. In 1567 Pope Pius V sent him to the Far East to exercise his Episcopal ministry in China and Japan. He arrived in Macau in 1568 and soon helped to set up the Senado (Town Council). In the following year, he established the Santa Casa da Misericordia (Holy House of Mercy), a charitable association which founded the present St. Raphael’s Hospital, the Leper Asylum of St. Lazarus, and an orphanage.
Nunes tried to open missions in mainland China. He went to Canton twice in 1576, but it was only in 1584 that the mission was finally established through the work of Fr. A. Valignano (1538-1606), M. Ruggieri (1545-1607), and M. Ricci (1552-1610). In 1579, he welcomed to Macau the first Franciscan fathers and in the following year he ordained five Jesuit priests. He retired in 1581, when the first appointed bishop of Macau, Leonardo Fernando de Sa (?-1587), arrived.